Biology subjects

White, S.

Publications and source records attributed to White, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Foodscapes for Salmon and Other Mobile Consumers in River Networks

Mobile consumers track fluctuating resources across heterogeneous landscapes to grow and survive. In river networks, the abundance and accessibility of food and the costs of foraging vary between habitats and through time, providing a shifting mosaic of growth opportunities for mobile consumers. However, a framework integrating the spatiotemporal dynamics of growth potential within riverscapes has been lacking. Here we present the concept of "foodscapes" to depict the dynamic changes in food abundance, food accessibility, and foraging costs that contribute to spatial and temporal variation of fish growth in rivers. Drawing on case studies of salmonid fishes from Alaska to California, we illustrate that "healthy" foodscapes provide a plethora of foraging opportunities--promoting diverse life history strategies that potentially enhance population stability. We identify knowledge gaps in understanding foodscapes, and approaches for management that focus on restoring trophic pathways which support diverse foraging and growth opportunities for fish in river networks.

ecology↗

bioRxiv2023

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. While tools exist to answer this question, all existing approaches to date return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, no tools to date account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. In this work, we present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of average nucleotide identity, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power as well as quantify theoretically how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. Code implementing this approach, as well as all experiments performed, is available at https://github.com/KoslickiLab/YACHT.

bioinformatics↗

bioRxiv2022

Development of Enterovirus anti-viral agents that target the viral 2C protein

The enterovirus (EV) genus includes a number of important human and animal pathogens. EV-A71, EV-D68, poliovirus (PV), and coxsackievirus (CV) outbreaks have affected millions worldwide causing a range of upper respiratory, skin, neuromuscular diseases, including acute flaccid myelitis, and hand-foot-and-mouth disease. There are no FDA-approved anti-viral therapeutics for these enteroviruses. In this study, we describe novel broad spectrum anti-viral compounds targeting the conserved non-structural viral protein 2C that have low micro-molar to nanomolar IC50 values. The selection of resistant mutants resulted in amino acid substitutions in the viral capsid protein, implying a role for 2C in capsid assembly, as has been seen in PV. The assembly and encapsidation stages of the viral life cycle are not fully understood and the inhibitors reported here could be useful probes in understanding these processes.

pharmacology and toxicology↗

bioRxiv2022

The wild life of ticks: using passive surveillance to determine the distribution and wildlife host range of ticks and the exotic Haemaphysalis longicornis, 2010-2021

BackgroundWe conducted a large-scale, passive regional survey of ticks associated with wildlife of the eastern U.S. Our primary goals were to better assess the current geographic distribution of exotic H. longicornis and to identify potential wild mammalian and avian host species. However, this large-scale survey also provided valuable information regarding the distribution and host associations for many other important tick species that utilize wildlife as hosts. MethodsTicks were opportunistically collected by cooperating state and federal wildlife agencies. All ticks were placed in the supplied vials and host information was recorded, including host species, age, sex, examination date, location (at least county and state), and estimated tick burden were recorded. All ticks were identified to species using morphology, suspect H. longicornis were confirmed through molecular techniques. ResultsIn total, 1,940 hosts were examined from across 369 counties from 23 states in the eastern U.S. From these submissions, 20,626 ticks were collected and identified belonging to 11 different species. Our passive surveillance efforts detected exotic H. longicornis from nine host species from eight states. Notably, some of the earliest detections of H. longicornis in the U.S. were collected from wildlife through this passive surveillance network. In addition, numerous new county reports were generated for Amblyomma americanum, A. maculatum, Dermacentor albipictus, D. variabilis, and Ixodes scapularis. ConclusionsThis study provided data on ticks collected from animals from 23 different states in the eastern U.S. between 2010 - 2021 with the primary goal of better characterizing the distribution and host-associations of the exotic tick H. longicornis; however new distribution data on tick species of veterinary or medical importance was also obtained. Collectively, our passive surveillance has detected numerous new county reports for H. longicornis as well as I. scapularis. Our study utilizing passive wildlife surveillance for ticks across the eastern U.S. is an effective method for surveying a diversity of wildlife host species allowing us to better collect widespread data on current tick distributions relevant to human and animal health.

ecology↗

bioRxiv2022

HSV Tegument Protein pUL51 Interacts with Host Dynactin for Viral Spread

Dynein motors are microtubule associated protein complexes that mediate multiple essential cellular processes, such as long-distance cargo trafficking and stabilization of the microtubule organization center. Most of these functions and their regulations depend on the dynein motor subunit dynactin. By using an infection-inducible system, we disrupted dynein motor function after HSV entry by overexpressing a dominant-negative inhibitor of dynein, resulting in a 5-fold growth defect in Vero cells and 1000-fold growth defect in CAD neuronal cells. Also, we found that in infected CAD cells, the dynein complex was recruited to viral assembly sites regardless of microtubule polymerization. Based on these observations, we then identified a novel interaction between conserved HSV-1 tegument protein pUL51 and p150Glued. pUL51 is a palmitoylated Golgi membrane-associated protein that is required for efficient virus assembly and spread. Overexpression of pUL51 alone was sufficient to recruit p150Glued to Golgi membranes. Sequences that are important and sufficient for pUL51-p150Glued interaction were mapped to residues 90 to 124 in pUL51 and residues 548 to 911 in p150Glued. Deletion of a.a 90-124 in pUL51 resulted in a moderate viral growth defect, a profound spread defect, and failure to accumulate both dynactin and the viral spread factor glycoprotein E (gE) at cell-cell junctions. A synthetic peptide that contains pUL51 a.a 90-125 could also inhibit viral growth and spread in pUL51-dependent manner. Taken together, our results suggest that the proper function of pUL51 in efficient viral assembly and spread depends on its interaction with p150Glued. Author SummaryDuring their life-long infections, herpesviruses can spread within the human body in spite of a powerful immune response that includes antibodies that inactivate the virus. The virus accomplishes this by targeting its newly made infectious particles to junctions where infected cells meet their uninfected neighbors. Junctional targeting of virus particles requires that the virus hijack normal cellular machinery used for moving large cargoes within the cell, a process that is only partially understood. In this study, we have discovered a critical interaction between a virus protein that is present in all herpesviruses and a host cell cargo-moving protein that is required for virus spread between cells and shown that this interaction is common to several medically important human herpesviruses. We have also identified a short piece of this virus protein that is responsible for the interaction and shown that this short piece can be used to interrupt the interaction and prevent spread of herpes simplex virus (HSV) in cultured cells. Our study provides prove-of-concept evidence that the spread pathway of HSV, and possibly other herpesviruses, can be targeted for therapeutic purposes.

cell biology↗

bioRxiv2021

SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2 infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named vmiR-5p (for viral miRNA), derived from the SARS-CoV-2 ORF7a transcript. Its abundance ranges from low to moderate as compared to host miRNAs. vmiR-5p functionally associates with Argonaute proteins -- core components of the RNA interference pathway -- leading to downregulation of host transcripts. One such host messenger RNA encodes Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which is linked to interferon signaling. We demonstrate that vmiR-5p production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence. Significance statementWe discovered that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses a small viral non-coding RNA, named vmiR-5p (for viral miRNA), derived from the ORF7a transcript. vmiR-5p associates with the cellular RNA interference machinery to regulate host transcripts likely via target silencing. The production of vmiR-5p relies on cellular machinery and the formation of a strong hairpin within ORF7a sequences. This newly-described vmiR-5p may contribute to SARS-CoV-2 pathogenesis and could become a target for therapeutic intervention.

microbiology↗

bioRxiv2021

Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi)

Tanner crab (Chionoecetes bairdi) are an economically important species that is threatened by ocean warming and Bitter Crab Disease, which is caused by an endoparasitic dinoflagellate, Hematodinium. Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To provide a transcriptomic resource for the Tanner crab, we generated a suite of RNA-seq libraries encompassing pooled hemolymph samples from crab displaying differing infection statuses and maintained at different temperatures (ambient (7.5{degrees}C), elevated (10{degrees}C), or decreased (4{degrees}C)). After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection, and detected some of those genes over time at the individual level using RNAseq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm.

physiology↗

bioRxiv2021

A two-year study on the phenology, host and habitat associations, and pathogens of Haemaphysalis longicornis in Virginia, U.S.A.

Understanding the abiotic and biotic variables affecting tick populations is essential for studying the biology and health risks associated with vector species. We conducted a study on the phenology of exotic Haemaphysalis longicornis (Asian longhorned tick) at a site in Albemarle County, Virginia. We assessed the importance of available wildlife hosts, habitats, and microclimate variables such as temperature, relative humidity, and wind speed on this exotic ticks presence and abundance. In addition, we determined the prevalence of selected tick-borne pathogens potentially transmitted by H. longicornis. We determined that the seasonal activity of H. longicornis was slightly different from previous studies in the northeastern United States. We observed nymphal ticks persist year-round but were most active in the spring, followed by a peak in adult activity in the summer and larval activity in the fall seasons. We also observed a lower probability of detecting H. longicornis in field habitats and the summer months. In addition, we detected H. longicornis on several wildlife hosts, including coyote (Canis latrans), eastern cottontail (Sylvilagus floridanus), raccoon (Procyon lotor), Virginia opossum (Didelphis virginiana), white-tailed deer (Odocoileus virginianus), woodchuck (Marmota monax), and a Peromyscus sp. This is the first detection of this tick on a rodent host important to the epidemiology of tick-borne pathogens of humans and animals. Finally, we continued to detect the exotic piroplasm parasite, Theileria orientalis Ikeda, in H. longicornis as well as other pathogens, including Rickettsia felis, Anaplasma phagocytophilum (AP-1), and a Hepatozoon sp. previously characterized in Amblyomma americanum. These represent some of the first detections of arthropod-borne pathogens native to the United States in host-seeking H. longicornis. These data increase our understanding of H. longicornis biology in the United States and provide valuable information into the future health risks associated with this tick and pathogens.

ecology↗

bioRxiv2021

Comparing instance segmentation methods for analyzing clonal growth of single cells in microfluidic chips

Appropriately tailored segmentation techniques can extract detailed quantitative information from biological image datasets to characterize and better understand sample distributions. Practically, high-resolution characterization of biological samples such as cell populations can provide insights into the sources of variance in biomarker expression, drug resistance, and other phenotypic aspects, but it is still unclear what is the best method for extracting this information from large image-based datasets. We present a software pipeline and comparison of multiple image segmentation methods to extract single-cell morphological and fluorescence quantitation from time lapse images of clonal growth rates using a recently reported microfluidic system. The inputs in all pipelines consist of thousands of unprocessed images and the outputs are the detection of cell counts, chamber identifiers, and individual morphological properties of each clone over time detected through multi-channel fluorescence and bright field imaging. Our conclusion is that unsupervised learning methods for cell segmentation substantially outperform supervised statistical methods with respect to accuracy and have key advantages including individual cell instance detection and flexibility through model training. We expect this system and software to have broad utility for researchers interested in high-throughput single-cell biology.

bioengineering↗

bioRxiv2020

Optimising biomedical relationship extraction with BioBERT: Best practices for data creation

Text mining is widely used within the life sciences as an evidence stream for inferring relationships between biological entities. In most cases, conventional string matching is used to identify cooccurrences of given entities within sentences. This limits the utility of text mining results, as they tend to contain significant noise due to weak inclusion criteria. We show that, in the indicative case of protein-protein interactions (PPIs), the majority of sentences containing cooccurrences ({bsim}75%) do not describe any causal relationship. We further demonstrate the feasibility of fine tuning a strong domain-specific language model, BioBERT, to analyse sentences containing cooccurrences and accurately (F1 score: 88.95%) identify functional links between proteins. These strong results come in spite of the deep complexity of the language involved, which limits the accuracy even of expert curators. We establish guidelines for best practices in data creation to this end, including an examination of inter-annotator agreement, of semisupervision, and of rules based alternatives to manual curation, and explore the potential for downstream use of the model to accelerate curation of interactions in the SIGNOR database of causal protein interactions and the IntAct database of experimental evidence for physical protein interactions.

bioinformatics↗

bioRxiv2020

Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome

The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

pathology↗

bioRxiv2020

Isolating Compounds that Inhibit EV 71 Virus

Enterovirus 71, or EV 71, is responsible for causing Hand, Foot, and Mouth disease in humans. In particular, it is especially deadly when children and small infants are exposed. The objective of this research paper is to address the possibility of a novel antiviral drug that can be used once infection of EV 71 has occurred. The methods for this research include transformation of E. coli with the genetic information from Enterovirus 71, growth of the E. coli colonies in the lab setting, 2C protein purification, and ATPase assays with drug testing. Of the 364 drugs tested in the ATPase assay, a combination of two of them (Mitrofudil and N6-Benzyladenosine) indicated a stoppage in activity of ATPase, signaling no further activity of the enzyme and viral proliferation.

cell biology↗

bioRxiv2020

Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images

BackgroundImmunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are themselves organized into densely packed higher-level anatomical structures. These types of images can be challenging to segment automatically for several reasons, including the relevance of biomedical context, dependence on the specific set of probes used, prohibitive cost of generating labeled training data, as well as the complexity and dense packing of anatomical structures in the image. The use of an application ontology surmounts these challenges by combining image data with its metadata to provide a meaningful biological context, and hence constraining and simplifying the process of segmentation and object identification. ResultsWe propose an innovative approach for the automated analysis of complex and densely packed anatomical structures from immunofluorescent images that utilizes an application ontology to provide a simplified context for image segmentation and object identification. We describe how the logical organization of biological facts in the form of an ontology can provide useful constraints that enhance automatic processing of complex images. We demonstrate the results of ontology-guided segmentation and object identification in mouse developmental lung images from the Bioinformatics REsource ATlas for the Healthy lung (BREATH) database of the Molecular Atlas of Lung Development (LungMAP1) program. ConclusionThe microscopy analysis pipeline library (micap) is available at https://github.com/duke-lungmap-team/microscopy-analysis-pipeline. Code to reproduce our analysis of LungMAP images is also available at https://github.com/duke-lungmap-team/lungmap-pipeline. Finally, the application ontology is available at https://github.com/duke-lungmap-team/lung_ontology and includes example SPARQL queries. ContactAnna Maria Masci email: annamaria.masci@duke.edu

bioinformatics↗

bioRxiv2020

Natural Genetic Variation in Drosophila melanogaster Reveals Genes Associated with Coxiella burnetii Infection

The gram-negative bacterium Coxiella burnetii is the causative agent of Query (Q) fever in humans and coxiellosis in livestock. Association between host genetic background and Coxiella burnetii pathogenesis has been demonstrated both in humans and animals; however, specific genes associated with severity of infection remain unknown. We employed the Drosophila Genetics Reference Panel to perform a genome-wide association study and identify host genetic variants that affect Coxiella burnetii infection outcome. The analysis resulted in 64 genome-wide suggestive (P < 10-5) single nucleotide polymorphisms or gene variants in 25 unique genes. We examined the role of each gene in Coxiella burnetii infection using flies carrying a null mutation or RNAi knockdown of each gene and monitoring survival. Of the 25 candidate genes, 15 validated using at least one method. For many, this is the first report establishing involvement of these genes or their homologs with Coxiella burnetii susceptibility in any system. Among the validated genes, FER and tara play roles in the JAK-STAT, JNK, and decapentaplegic/TGF-{beta} signaling pathways that are associated with the innate immune response to Coxiella burnetii infection. Two other two validated genes, CG42673 and DIP-{varepsilon}, play roles in bacterial infection and synaptic signaling but no previous association with Coxiella burnetii pathogenesis. Furthermore, since the mammalian ortholog of CG13404 (PLGRKT) is an important regulator of macrophage function, CG13404 could play a role in Coxiella burnetii susceptibility through hemocyte regulation. These insights provide a foundation for further investigation of genetics of Coxiella burnetii susceptibility across a wide variety of hosts.

genetics↗

bioRxiv2020

HSV Forms an HCMV-like Viral Assembly Center in Neuronal Cells

Herpes simplex virus (HSV) is a neuroinvasive virus that has been used as a model organism for studying common properties of all herpesviruses. HSV induces host organelle rearrangement and forms dispersed assembly compartments in epithelial cells, which complicates the study of HSV assembly. In this study, we show that HSV forms a visually distinct unitary cytoplasmic viral assembly center (cVAC) in both cancerous and primary neuronal cells that concentrates viral structural proteins and is the site of capsid envelopment. The HSV cVAC also concentrates host membranes that are important for viral assembly, such as Golgi- and recycling endosome-derived membranes. Lastly, we show that HSV cVAC formation and/or maintenance depends on an intact microtubule network and a viral tegument protein, pUL51. Our observations suggest that the neuronal cVAC is a uniquely useful model to study common herpesvirus assembly pathways, and cell-specific pathways for membrane reorganization. SummaryThis study shows that HSV forms a viral assembly center in neuronal cells by reorganization of host membranes. This system is a novel and powerful tool to study herpesvirus assembly pathways and host cell membrane dynamics.

cell biology↗

bioRxiv2020

Structures of three actinobacteriophage capsids: Roles of symmetry and accessory proteins

Mycobacterium tuberculosis and abscessus are major human pathogens that are part of the Actinobacteria phylum. Increasing multiple drug resistance in these bacteria has led to a renewed interest in using viruses that infect these bacteria for therapy. In order to understand these viruses, a course-based undergraduate research experience (CURE) program run by SEA-PHAGES at the University of Pittsburgh and HHMI has isolated, sequenced, and annotated over 3000 actinobacteriophages (viruses that infect Actinobacteria). Little work has been done to investigate the structural diversity of these phage, all of which are thought to use a common protein fold, the HK97-fold, in their major capsid protein. Here we describe the structure of three actinobacteriophage capsids isolated by students that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately 6 angstroms, which allowed confirmation that each phage uses the HK97-fold to form their capsid. One phage, Rosebush, has a novel variation of the HK97-fold. Four novel accessory proteins, that form the capsid head along with the major capsid protein, were identified that show limited or no homology to known proteins. The genes that encode the proteins were identified using SDS-PAGE and mass spectrometry. Bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

microbiology↗

bioRxiv2019

Geldanamycin inhibits Jumonji histone lysine demethylase KDM4 and targets chimeric transcription factor PAX3-FOXO1

Histone lysine demethylases (KDMs) are emerging as therapeutic targets in cancer. Development of potent KDM inhibitors may provide additional options for epigenomics-oriented therapies. Using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) functional demethylation assay, in combination with a high-content immunofluorescence imaging phenotypic screen, Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance mass spectrometry (MALDI-FTICR MS) and Amplified Luminescent Proximity Homogeneous Assay (ALPHA), we identified geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), as a novel inhibitor of JmjC-domain containing demethylases such as KDM4B. We further found that geldanamycin can destabilize the PAX3-FOXO1 fusion oncoprotein, an Hsp90 client, which is a driver of clinically unfavorable alveolar rhabdomyosarcoma (aRMS). We then hypothesized that dual inhibition of PAX3-FOXO1 and epigenetic modifiers of aRMS would have synergistic antitumor activity. We repurposed the geldanamycin analog 17-DMAG to target aRMS and found that 17-DMAG significantly delays tumor growth, extends survival in xenograft mouse models, and inhibits expression of PAX3-FOXO1 targets and multiple oncogenic pathways including MYC, E2F and NOTCH. In addition, the combination of 17-DMAG with conventional chemotherapy or the bromodomain inhibitor JQ1 significantly enhances therapeutic efficacy. In summary, we have identified geldanamycin and 17-DMAG as dual KDM/Hsp90 inhibitors and 17-DMAG is efficacious against PAX3-FOXO1-driven rhabdomyosarcoma.

cancer biology↗

bioRxiv2019

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Among these, iLINCS is unique in scope and versatility of the data provided and the analytics facilitated. iLINCS (http://ilincs.org) is an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates analysis of user-submitted omics signatures of diseases and cellular perturbations in the context of a large compendium of pre-computed signatures (>200,000), as well as mining and re-analysis of the large collection of omics datasets (>12,000), pre-computed signatures, and their connections. Analytics workflows driven by user-friendly interfaces enable users with only conceptual understanding of the analysis strategy to execute sophisticated analyses of omics signatures, such as systems biology analyses and interpretation of signatures, mechanism of action analysis, and signature-driven drug repositioning. In summary, iLINCS workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures.

bioinformatics↗